ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements

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MetadadosDescriçãoIdioma
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorUMR5558-
Autor(es): dc.contributorInstitut Universitaire de France (IUF)-
Autor(es): dc.contributorUMR 203-
Autor(es): dc.creatorOliveira, Daniel S.-
Autor(es): dc.creatorFablet, Marie-
Autor(es): dc.creatorLarue, Anaïs-
Autor(es): dc.creatorVallier, Agnès-
Autor(es): dc.creatorCarareto, Claudia M.A.-
Autor(es): dc.creatorRebollo, Rita-
Autor(es): dc.creatorVieira, Cristina-
Data de aceite: dc.date.accessioned2025-08-21T21:33:06Z-
Data de disponibilização: dc.date.available2025-08-21T21:33:06Z-
Data de envio: dc.date.issued2025-04-29-
Data de envio: dc.date.issued2023-10-13-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1093/nar/gkad671-
Fonte completa do material: dc.identifierhttps://hdl.handle.net/11449/304073-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/304073-
Descrição: dc.descriptionTransposable elements (TEs) produce structural variants and are considered an important source of genetic diversity. Notably, TE-gene fusion transcripts, i.e. chimeric transcripts, have been associated with adaptation in several species. However, the identification of these chimeras remains hindered due to the lack of detection tools at a transcriptome-wide scale, and to the reliance on a reference genome, even though different individuals/cells/strains have different TE insertions. Therefore, we developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts through two different modes. Mode 1 is the reference-guided approach that employs canonical genome alignment, and Mode 2 identifies chimeras derived from fixed or insertionally polymorphic TEs without any reference genome. We have validated both modes using RNA-seq data from four Drosophila melanogaster wild-type strains. We found ∼1.12% of all genes generating chimeric transcripts, most of them from TE-exonized sequences. Approximately ∼23% of all detected chimeras were absent from the reference genome, indicating that TEs belonging to chimeric transcripts may be recent, polymorphic insertions. ChimeraTE is the first pipeline able to automatically uncover chimeric transcripts without a reference genome, consisting of two running Modes that can be used as a tool to investigate the contribution of TEs to transcriptome plasticity.-
Descrição: dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)-
Descrição: dc.descriptionConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)-
Descrição: dc.descriptionAgence Nationale de la Recherche-
Descrição: dc.descriptionSão Paulo State University (Unesp) Institute of Biosciences Humanities and Exact Sciences, SP-
Descrição: dc.descriptionLaboratoire de Biométrie et Biologie Evolutive Université Lyon 1 CNRS UMR5558, Rhone-Alpes-
Descrição: dc.descriptionInstitut Universitaire de France (IUF), Île-de-FranceF-
Descrição: dc.descriptionUniv Lyon INRAE INSA-Lyon BF2I UMR 203-
Descrição: dc.descriptionSão Paulo State University (Unesp) Institute of Biosciences Humanities and Exact Sciences, SP-
Descrição: dc.descriptionFAPESP: 2020/06238-2-
Descrição: dc.descriptionCNPq: 308020/2021-9-
Descrição: dc.descriptionAgence Nationale de la Recherche: ANR-14-CE19-0016-01-
Formato: dc.format9764-9784-
Idioma: dc.languageen-
Relação: dc.relationNucleic Acids Research-
???dc.source???: dc.sourceScopus-
Título: dc.titleChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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